Ghosts
by F-14 Tomcat Lover
Summary: Two brothers lived in peace. Now one's secrets have begun to spill and the other is learning the secrets of his true past. Thrust into a war held in the shadows, can Kira Yamato and company find out the truth or will death be there last move? AU


Disclaimer: I do not own Gundam SEED.

Summary: Kira Yamato thought that he was just an average young man. True he was very gifted in science and computers, but that was about it. He lived with his elder half brother on Heliopolis, but then some men began to chase him and his brother. What is the real story behind not only himself, but also his brother? This is an AU.

"_**Ghosts"**_

_**Phase One: "The Beginning" **_

**_Be Born and Rise Up Gundam!_**

**Heliopolis Central Park, Area 3B, Heliopolis, Orb Union**

**January 17th, 72nd Year of the Cosmic Era**

A brown haired, violet-eyed young man was typing away at his laptop as he listened to a speech given by his elder brother about the need to reform the United Nations and to recognize the PLANTS independence. He was watching a video stream on his laptop as he worked. At the same time stretched lazily across the bench they were on was his girlfriend Mirillia Haw with her head resting on his lap.

He still wondered how the two had become so close so fast. He still remembered it was his best buddy and Mirillia's first boyfriend, Tolle Koenig that took a burst of automatic fire meant for all three of them, but he took it alone. It was Blue Cosmos, as it always was, officially. They had been after a suspected First Generation Coordinator and had attacked the Heliopolis Technical Institute. Kira's elder brother, Jamie Yamato, had been there and knew how to use firearms. He had put a bullet, each, in the head of the four terrorists that tried to kill Kira and Mirillia, but still got Tolle. Tolle had shielded the two and pushed them behind some cover, but in doing so he was left exposed and off balanced. Later, it turned out that they had chased after just a highly intelligent Natural with a big ego, but that was only one reason why schools refused to acknowledge the great achievements of their students anymore, anywhere, anytime.

Kira sighed as he often did when thinking about his school life. He was 17 years old closing in on his eighteenth birthday, but he had to be anonymous. His brother on the other had nearly become an Orb Special Forces soldier, with his own command, because of a natural talent at being such a person. Jamie on the other hand, politely refused and decided to just be a normal security guard, but now he was famous throughout the sphere as a vocal advocate for the reformation of the United Nations and the war on terrorism. Kira often wondered about his brother, but decided to drop it, he had work to finish, and then Mirillia and him were going shopping for a new bikini for her.

Kira chuckled to himself, as he put a hand on her shoulder. She was sound asleep with her head on his lap. Usually it was the other way around, but he didn't mind about the change. That was when he heard the gentle tell tale flapping of his mechanical bird Tori and then the strong whoosh of a mechanical hawk over came Tori's gentle flap. Both landed in front of Kira.

"Tori, Silver, how are you two today?" Kira asked the birds as he gave each a gentle pat.

"Birdie!" Tori answered happily and excitedly, meaning he was fine and happy.

Silver gave a few gentle chirps that meant the same thing. Kira would never know why his brother insisted that anything that Athrun Zala had made for him be real close to real as can be. In this case, a mechanical hawk soundly like a real hawk. Though no one wonders why, after all unlike Kira, Jamie had started growing up on Earth before moving to space, so it would be understandable that he was probably homesick for it.

The gentle chirps woke Mirillia up and she looked up to see the familiar sight of the Yamato Brothers two mechanical birds. She sat up and stretched and yawned and allowed Silver to climb onto her arm and Tori her shoulder. Mirillia really liked playing with the two brothers' birds. She especially liked the way they could deliver messages to and from, especially when they were to and from Kira.

Mirillia then noticed Kira with a small smile on his face. He was happy that she was happy being with him and the two birds. Mirillia knew that Kira longed to know his father and their mother, but Jamie never talked about it. So when Mirillia and Kira became close a year ago, it filled an empty void in Kira's heart and soul. And both couldn't be happier.

Mirillia leaned in and the two shared a kiss. It would have gone further had someone not cleared their throat. The two looked up to see Sai Argyle and Flay Allster, a couple of their friends. The two looked embarrassed and Kira went right back to work as his girlfriend and two friends talked. Once finished, the four headed to a small, but likeable place that carried high quality swimming outfits at very reasonable and cheap prices. Then they headed to the beach where Mirillia swam in her new yellow sunflower colored two-piece bikini with red trim and white stripes. Then as it grew late in the afternoon, they all decided to head to the home of the Yamato brothers to rest and shower and then do the things that a lot of seventeen year olds do.

That night, Kira had another of his nightmares. He began to thrash about; his unkempt brown hair was slick with perspiration. He thrashed about in bed. Mirillia who had stayed over too late into the night with Sai and Flay heard him screaming in his sleep. He was calling out for his parents.

Jamie who had just return seconds before Kira started screaming ran up to his room. At once the older sibling tried to calm his brother. He was partially successful, but Kira still thrashed. It wasn't until Mirillia began to hold him close that he finally stopped thrashing. He calmed down and was soon fast asleep.

Chasing Sai and Flay out of the room and closing the door behind him. Jamie rubbed the bridge of his nose. He knew Kira always had these nightmares. The fact ate at his very soul, but he knew he must keep his silence just a little longer, at least for now. He motioned for Sai and Flay to sit down on the living room couch. Flay's steel blue eyes and Sai's honey brown eyes looked at the brown haired Prussian eyed man.

"Don't ever repeat anything about this outside of this building," Jamie was to the point as always.

"What do you mean?" Flay asked.

"Our parents, as far as Kira knows, were separated from us by a Blue Cosmos attack," everyone knew what he said, but Sai caught on to the middle part.

"Then what really happened?" Sai asked.

"They were killed by Blue Cosmos and I was too weak to save them," Jamie answered not even looking at them.

"I see, so Kira is a Coordinator then?" Sai asked, believing he was right.

"No, a Natural… He was born with violet eyes, if you look into rare medical conditions, you will find that for years there have been cases of people born with unique eye color. I remember the last person born with violet eyes was about twenty-thirteen of the old calendar. Another young woman with blonde hair was reported to have purple eyes a shade darker than Kira's, but that is recent and she vanished, no doubt murdered by Blue Cosmos, but she was a Natural," Jamie had done his homework well.

"But why would Blue Cosmos attack her?" Flay was confused.

"There's an old line that I found during my studies. 'Those that use terror have an eye problem…'" he started.

"An eye problem?" Flay/Sai said.

"… When it comes to identifying friend from foe,'" he finished.

"You mean that because she had unusual eyes she was mistaken for a Coordinator, but how, aren't they usually diligent about that?" Sai knew that Blue Cosmos was crazy, but that took the cake.

"They don't care, they even tried to murder Princess Athha on several occasions, even though it is a known fact that she is a Natural with a less rare eye color, amber, I actually had them when I was born, but it went away after several years, before Kira's father met mother," Jamie was as cool as a snow fall in winter.

"I see, so he is just one of those who are very highly skilled, but isn't a Coordinator," Sai said feeling better, though even if Kira were a Coordinator, he wouldn't care, because Kira would still be Kira.

It was at that time, Flay realized how she was dress. She was in a pink bra and pink panties only and noticed that Sai was just in his boxers and undershirt. Flay did what was natural to women, she screamed bloody murdered with a face redder than her fiery locks of hair and slapped both males before disappearing into the guest room.

"What was that about?" Jamie was shocked, but Sai realized it.

"Umm… She was only in her underwear," he said with a blush.

"Hn… I didn't notice," Sai just about fell over as Jamie took a drink of his coffee he had.

"Thank the Goddess for small favors," he said after he finished the coffee.

"How come?" Sai was curious.

"Most coffee has a metallic taste that includes the taste of machine oil and other things, but I found this guy that makes real fine coffee. He can turn anyone who hates coffee into a coffee nut and lover," he put the mug into the sink and yawned and told Sai to go back to bed as he went to his room to ready himself for bed.

In Kira's room, Mirillia stayed next to Kira. He had woken up a bit and Mirillia knew from the sheer look of terror in his eyes that it had been one hell of a nightmare. She kissed him to calm him, but she then slipped him out of his undershirt and then she laid down next to him, placing her head down on his bare shoulder. She held him close and with a small blush.

Kira kissed the top of her head and fell to sleep. The direct warmth of her body was soothing his frightened soul. He fell into a sleep void of nightmares, but full of happy dreams. Even as he entered the world of sleep, he felt Mirillia also fall to the land of sleep.

* * *

Across the street several men in black moved towards the small house. Their orders were clear. Eliminate a Coordinator and a Sympathizer that lived with him. Their orders gave priority to the Sympathizer, because he was beginning to undermine Blue Cosmos's power. He was a greater threat than the whole of the Zodiac Alliance of Freedom Treaty. Unfortunately for them, they arrived, only to have the house explode in their faces.

They watched in stunned surprise as a car zoomed passed them and off into the night. They had seen a rocket launcher being stored and a man on a radio. It was obvious that they were professionals. Yet a questioned remained as they started to flee for their lives, who were they?

* * *

Driving nearly inhumanly fast towards a secret dock hidden in one of the old storage sites located in an older area of Heliopolis, Jamie looked over the still sleepy group of kids. Jamie knew it had only been a couple of hours since everyone had fallen back to sleep after Kira's nightmare work them all up. He had awoken when an old feeling that he had long come to rely on told him of an impending attack. It was a good thing too and after all, he wasn't just another average Natural with soldier like skills.

The four kids began to nod off as Jamie looked back into the rearview mirror to see his and Kira's home now going up in smoke. He couldn't actually see it, but he knew the area from where the smoke was, that their home was gone. He sighed and decided to rouse the kids, as they would soon be at their destination.

"Kira, Mir, Flay, Sai, sorry to do this, but there is no more time to sleep now, later yes, if we're lucky," Jamie said with an authoritive voice.

The four teens began to awaken a little again, but were still very sleepy. Jamie knew they needed to be awake as they were fast approaching their destination. If they didn't awake now, they would end up with eternal sleep and that he would not allow.

"I said wake up or would you rather be killed in your sleep?" he said with a very sharp edge to his voice and the four were awake, as Jamie Yamato never spoke like that.

"Brother what's going on?" Kira asked.

"I don't know who, but I have a good guess, just blew our home away Kira. We no longer have a house here on Heliopolis," Jamie said his voice calming.

"WHAT?" the younger brother exclaimed.

"Its not time yet to talk Kira, but I promise you someday I will…" a bullet hit Jamie in the chest, but amazingly he kept control of the car.

"BROTHER!" Kira yelled.

"Its not as bad as you think Kira," Jamie's voice was weak as Silver began to call to its master from the back seat.

"I'll be fine once we get to our escape route," he replied.

"Brother?" Kira began unsure.

"Mir, Sai, and Flay, sorry to involve you, but now is not the time for an useless debate or discussion. We need to get the hell out of dodge and to somewhere safe," Jamie was feeling his vision start to blur, but he held firm and drove on.

"What's happening?" Sai asked, confused.

"An attack… to be more precise an attempt to assassinate Kira and myself… I've done more than just advocate for the restoration of the UN… In reality, some have already reformed it and I command a Special Forces unit for the United Nations Peace Keeping Squadron Number three-eighty-five, the Hammer of Thor Squadron…" Jamie was losing it, but he pressed on.

"Don't talk Jamie," Mirillia said.

"Listen, we're abandoning Heliopolis since my enemies have found me, found us… My shuttle will take us to safety… Inside is a gift for you Kira… Then when I am better, we will talk…" Jamie was nearing the end of his strength.

They soon arrived at the secret dock for the shuttle. They quickly abandon the car and fled inside, just a rocket landed near the car, sending it flying and flipping a few meters into the air, before it came back down with a crunching of metal and a minor explosion from the fuel cell. The car was totaled and destroyed. No amount of work would be able to repair that wreck.

Once inside, Jamie led them to a secret underground area and there opened up an old hatch and physically threw the four youngsters and some few belongings they had grabbed on the way out of the house into the shuttle and then ordered the two mechanical birds follow. Kira was the first back up as the hatched closed. He saw his brother shooting at someone, dropping them. Then he turned and gave a faint smile. Kira saw that he had incurred more wounds. Then he reached over and hit a button. The shuttle was then launched from the hidden docking bay, Kira screaming for his brother as the docking area was engulfed in flames and people could be seen floating out into the vastness of space without protection.

"JAMIE!" Kira shouted at the top of his lungs as the shuttle's engines kicked on and the craft huddled into space and away from the colony that he and his three friends called home.

Almost at once, Heliopolis Defense Force Mobile Pods were on the scene, but they missed the shuttle. On the interior, the wreck car had been found. Checking for ownership, they found that Jamie Yamato owned the once green four door family car. They also found Jamie Yamato in the wreckage of the docking bay interior an empty automatic pistol in his hand.

Inside the shuttle, Kira and the others just floated. They all noticed the bits of blood that had ended up in the shuttle. The hatch had a fair amount. The birds did not move, as they seemed to be mourning the loss of Jamie Yamato. He felt Mirillia's arms circle around him and he knew she was crying, they were all crying.

Then a noise alerted them to the bridge. There they found the shuttle on autopilot, but it seemed to have a blinking light meant for something. Kira touched it and it began to play.

"_K… Kira… this… this… message may be somewhat… when you… it…I will…about…parents… the… you… shall have… I promised… keep it… Truth is… are… brothers…I… to you… to protect you… from… many who wish to use or kill you Kira… You are a Coordinator… First… Generation…but…not…all… You… Yamato… are the Ultimate Coordinator… A… above… all other Coordinators… Seek out… he… will tell you… more… your sister as… Kira… you may not…been my… brother… by blood… but you will always be my little brother… If you want more… answers… seek out… Colony… Lagrange Point Four… seek out… R and D… I love you Kira, as a brother should and I leave the Shuttle _Brotherly Love_ to you and the mobile suit, ZGMF-X10A Freedom… I stole it… from… ZAFT… to keep it… out of…hands… use it… wisely my brother… Money can be found in a… blind… trust… fund… under… Lance Halberton… my real name..."_

Kira knew the static filled message was degraded, but then saw the static filled pictured of the ZGMF-X10A Freedom in the back storage bay which hadn't degraded as much. His eyes widened at the sight of the mobile suit. A mobile suit that now belonged to him. With a shuttle and friends with him, he now had a set goal in life. He was going to discover the truth of his life and of those that took his brother's life.

As Kira sat in the pilot's seat, many a thought ran through his head. He saw Mirillia taking the Co-pilot's seat as Flay took communications and Sai the Flight Engineer's post. The most important thing right now was to find out about his sister he never knew he had and why Jamie wasn't his real brother. Still, despite not being blood brothers, Jamie was his brother. Now he plans to set out with his three friends to find out who was behind this and to topple them. He would carry out his brother's dream of peace and freedom.

* * *

Okay, this is a new story that just came to me and I had to write it. I decided on a little different out take with this story. I also decided to toy with a Kira/Mirillia story. It may change so don't hold me to it. It could change and become a Kira/Lacus, Kira/Flay (Heaven Forbid, just kidding), Kira/Meryin, Kira/Luna, Kira/Shiho (yes, I may experiment), Kira/Stellar, and finally Kira/OC. I might even change things like Cagalli being Kira's twin and make that into Stellar being Kira's twin sister so that I can write a Kira/Cagalli, but that is a rather big IF.

So I'm asking, send in your votes ladies and gentlemen. For your favorite pairing for not only Kira, but for the other characters, but note, this is a limited time offer, so hop to it! Don't delay!

Maybe I should cut back on the TV a lot.


End file.
